Tetsuo Shibuya's publications

Please feel free to contact me at tshibuya 'at-mark' hgc 'dot' jp to request copies of papers whose files are not provided.

Refereed Journal Papers

Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, and Susumu Goto, Revealing Phenotype-Associated Functional Differences by Genome-Wide Scan of Ancient Haplotype Blocks, PLOS ONE, April 26, 2017, https://doi.org/10.1371/journal.pone.0176530.
Kiyoshi Yamaguchi, Satoshi Nagayama, Eigo Shimizu, Mitsuhiro Komura, Rui Yamaguchi, Tetsuo Shibuya, Masami Arai, Seira Hatakeyama, Tsuneo Ikenoue, Masashi Ueno, Satoru Miyano, Seiya Imoto, Yoichi Furukawa, Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis, Scientific Reports 6, Article number: 26011, 2016, doi:10.1038/srep26011.
Akihiro Fujimoto, Mayuko Furuta, Yasushi Totoki, Tatsuhiko Tsunoda, Mamoru Kato, Yuichi Shiraishi, Hiroko Tanaka, Hiroaki Taniguchi, Yoshiiku Kawakami, Masaki Ueno, Kunihito Gotoh, Shun-ichi Ariizumi, Christopher P Wardell, Shinya Hayami, Toru Nakamura,Hiroshi Aikata, Koji Arihiro, Keith A Boroevich, Tetsuo Abe, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Ayako Ohsawa, Tetsuo Shibuya, Hiromi Nakamura, Natsuko Hama, Fumie Hosoda, Yasuhito Arai, Shoko Ohashi, Tomoko Urushidate, Genta Nagae, Shogo Yamamoto, Hiroki Ueda, Kenji Tatsuno, Hidenori Ojima, Nobuyoshi Hiraoka, Takuji Okusaka, Michiaki Kubo, Shigeru Marubashi, Terumasa Yamada, Satoshi Hirano, Masakazu Yamamoto, Hideki Ohdan, Kazuaki Shimada, Osamu Ishikawa, Hiroki Yamaue, Kazuki Chayama, Satoru Miyano, Hiroyuki Aburatani, Tatsuhiro Shibata, and Hidewaki Nakagawa, "Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer", Nature Genetics 48, 500–509, April 2016. doi:10.1038/ng.3547.
Wing-Kin Sung, Kunihiko Sadakane, Tetsuo Shibuya, Abha Belorkar and Iana Pyrogova, An O(m log m)-time algorithm for detecting superbubbles, IEEE/ACM Transactions on Computational Biology and Bioinformatcs, 12(4), pp. 770-777, July/August 2015. doi:10.1109/TCBB.2014.2385696
Yoichi Furukawa, Kiyoshi Yamaguchi, Mitsuhiro Komura, Rui Yamaguchi, Seiya Imoto, Eigo Shimizu, Shinichi Kasuya, Tetsuo Shibuya, Seira Hatakeyama, Norihiko Takahashi, Tsuneo Ikenoue, Keisuke Hata, Giichiro Tsurita, Masaru Shinozaki, Yutaka Suzuki, Sumio Sugano, and Satoru Miyano. Detection of APC mosaicism by next-generation sequencing in an FAP patient. Journal of Human Genetics, 60(5), pp. 227-231, DOI: 10.1038/jhg.2015.14, May 2015.
Yoichi Furukawa, Tsuneo Ikenoue, Kiyoshi Yamaguchi, Mitsuhiro Komura, Seiya Imoto, Rui Yamaguchi, Eigo Shimizu, Shinichi Kasuya, Tetsuo Shibuya, Seira Hatakeyama, and Satoru Miyano, Attenuated Familial Adenomatous Polyposis with Desmoids by an APC Mutation. Human Genome Variation, vol. 2, Article number: 15011, doi:10.1038/hgv.2015.11, 26 March 2015.
Akihiro Fujimoto, Mayuko Furuta, Yuichi Shiraishi, Ha Nguyen, Daichi Shigemizu, Kunihito Gotoh, Yoshiiku Kawakami, Toru Nakamura, Masaki Ueno, Shun-ichi Ariizumi, Tatstuhiro Shibata, Tetsuo Abe, Keith Boroevich, Kaoru Nakano, Aya Sasaki, Rina Kitada, Kazihiro Maejima, Hiroko Tanaka, Tetsuo Shibuya, Hidenori Ojima, Kazuaki Shimada, Shinya Hayami, Yoshinobu Shigekawa, Hiroshi Aikata, Koji Arihiro, Hideki Ohdan, Shigeru Marubashi, Terumasa Yamada, Osamu Ishikawa, Michiaki Kubo, Satoshi Hirano, Masakazu Yamamoto, Hiroki Yamaue, Kazuaki Chayama, Satoru Miyano, Tatsuhiko Tsunoda, and Hidewaki Nakagawa. Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity, Nature Communications 6, Article No. 6120, doi:10.1038/ncomms7120, 30 January 2015.
Yuichi Shiraishi, Akihiro Fujimoto, Mayuko Furuta, Hiroko Tanaka, Ken-ichi Chiba, Keith A Boroevich, Tetsuo Abe, Yoshi-iku Kawakami, Masaki Ueno, Kunihito Gotoh, Shun-ichi Ariizumi, Tetsuo Shibuya, Kaoru Nakano, Aya Sasaki, Kazuhiro Maejima, Rina Kitada, Shinya Hayami, Yoshinobu Shigekawa, Shigeru Marubashi, Terumasa Yamada, Michiaki Kubo, Osamu Ishikawa, Hiroshi Aikata, Koji Arihiro, Hideki Ohdan, Masakazu Yamamoto, Hiroki Yamaue, Kazuaki Chayama, Tatsuhiko Tsunoda, Satoru Miyano, and Hidewaki Nakagawa, Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers, PLoS ONE 9(12): e114263. doi:10.1371/journal.pone.0114263, December 2014.
Akihiro Fujimoto, Yasushi Totoki, Tetsuo Abe, Keith A Boroevich, Fumie Hosoda, Ha Hai Nguyen, Masayuki Aoki, Naoya Hoshono, Michiaki Kubo, Fuyuki Miya, Yasuhito Arai, Hiroyuki Takahashi, Takuya Shirakihara, Masao Nagasaki, Tetsuo Shibuya, Kaoru Nakano, Kumiko Watanabe-Makino, Hiroko Tanaka, Hiromi Nakamura, Jun Kusuda, Hidenori Ojima, Kazuaki Shimada, Takuji Okusaka, Masaki Ueno, Yoshinobu Shigekawa, Yoshiiku Kawakami, Koji Arihiro, Hideki Ohdan, Kunihito Gotoh, Osamu Ishikawa, Shun-ichi Ariizumi, Masakazu Yamamoto, Terumasa Yamada, Kazuaki Chayama, Tomoo Kosuge, Hiroki Yamaue, Naoyuki Kamatani, Satoru Miyano, Hitoshi Nakagama, Yusuke Nakamura, Tatsuhiko Tsunoda, Tatsuhiro Shibata, and Hidewaki Nakagawa. Whole Genome Sequencing of Liver Cancers Identifies Etiological Influences on Mutation Patterns and Recurrent Mutations in Chromatin Regulators. Nature Genetics, Vol. 44, pp. 760-764, 2012.
Mohammed Sahli and Tetsuo Shibuya, Arapan-S: A Fast and Highly Accurate Whole-Genome Assembly Software for Viruses and Small Genomes, BMC Research Notes, 5:243, doi:10.1186/1756-0500-5-243, 2012.
Genki Terashi, Tetsuo Shibuya, and Mayuko Takeda-Shitaka, LB3D: a protein 3D substructure search program based on the lower bound of a RMSD value, Journal of Computational Biology, Vol. 19, No. 5, pp. 493-503, 2012.
Mohammed Sahli and Tetsuo Shibuya, Max-Shift BM and Max-Shift Horspool: Practical Fast Exact String Matching Algorithms. Journal of Information Processing, Vol. 53, No. 4, 2012.
Ritsuko Onuki, Ryo Yamada, Rui Yamaguchi, Minoru Kanehisa, and Tetsuo Shibuya, Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering, Journal of Computational Biology, Vol. 19, No 1, pp. 55-67, 2012. (journal site)
Mohammed Sahli and Tetsuo Shibuya, Removing vector sequences from shotgun raw data. Journal of Biotechnology, Bioinformatics and Bioengineering, Vol. 4, pp. 431-441, 2011.
Akihiro Fujimoto, Hidewaki Nakagawa, Naoya Hosono, Kaoru Nakano, Tetsuo Abe, Keith A Boroevich, Masao Nagasaki, Rui Yamaguchi, Tetsuo Shibuya, Michiaki Kubo, Satoru Miyano, Yusuke Nakamura, and Tatsuhiko Tsunoda. Whole-genome Sequencing and Comprehensive Variant Analysis of a Japanese Individual Using Massively Parallel Sequencing, Nature Genetics, Vol. 42, pp. 931-936, 2010. (journal site)
Tetsuo Shibuya, Searching Protein 3-D Structures in Faster Than Linear Time, Journal of Computational Biology, Vol. 17, No. 4, pp. 593-602, 2010. (preprint) (journal site)
Tetsuo Shibuya, Fast Hinge Detection Algorithms for Flexible Protein Structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 2, 2010, pp. 333-341. (preprint) (journal site) (IPSJ Yamashita SIG Research Award, March 11, 2009)
Tetsuo Shibuya, Searching Protein 3-D Structures in Linear Time, Journal of Computational Biology, Vol. 17, No. 3, pp. 203-219, 2010. (Preliminary version has appeared in RECOMB '09) (journal site)
Tetsuo Shibuya, Geometric Suffix Tree: Indexing Protein 3-D Structures, Journal of the ACM, Vol. 57, No. 3, Article No.15, pp. 1-17, 2010.(ACM portal)
Tetsuo Shibuya, Jesper Jansson, and Kunihiko Sadakane, Linear-Time Protein 3-D Structure Searching with Insertions and Deletions, BMC Algorithms for Molecular Biology, Vol. 5:7, 2010. (journal site) (PDF file at the journal site)
Ben Hachimori and Tetsuo Shibuya, Lazy Suffix Array: The Data Structure for Online Construction and Pattern Searching, IEICE Transactions on Fundamentals, Vol. E92-A, No. 8, pp. 1750-1756, 2009. (J-Stage)
Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, Journal of Computational Biology, Vol. 14, No. 9, pp. 1201-1207, 2007. (journal site) (preprint)
Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern Matching, Algorithmica, Vol. 39, No. 1, pp. 1 - 19, 2004. (journal site) (preprint)
Tetsuo Shibuya, Hisashi Kashima, and Akihiko Konagaya, Efficient Filtering Methods for Clustering cDNAs with Spliced Sequence Alignment, Bioinformatics, Vol. 20, pp. 29-39, 2004. (journal site)
Eain Murphy, Isidore Rigoutsos, Tetsuo Shibuya, and Thomas Shenk, Re-evaluation of Human Cytomegalovirus Coding Potential, Proceedings of the National Academy of Sciences, Vol. 100, No. 23, pp. 13585-13590, 2003. (journal site)
Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, and Tetsuo Shibuya, The IBM Bioinformatics Group Web Server - Tools and Content, Nucleic Acids Research, Vol. 31, No. 13, pp. 3645-3650, 2003. (journal site)
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol. E86-A, No.5, pp. 1061-1066, May 2003. (journal site) (PDF file)
Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Prokaryotic Gene Finding, Nucleic Acids Research, Vol. 30, pp. 2710-2725, 2002. (journal site) (PDF file)
Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, Algorithmica, Vol. 33, pp. 287-299, 2002. (journal site) (preprint)
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, The ACM Journal of Experimental Algorithmics, ISSN 1084-6654, Vol. 5, No. 9, 2000. (journal site) (PDF file)
Tetsuya Ueda, Hiroki Sasaki, Yoshitaka Kuwahara, Masahiko Nezu, Tetsuo Shibuya, Hiromi Sakamoto, Kazuyoshi Yanagihara, Kennichi Mafune, Masatoshi Makuuchi, and Masaaki Terada, Deletion of the Carboxyl-Terminal Exons of K-sam/FPGR2 by Short Homology-Mediated Recombination, Generating Preferential Expression of Specific mRNAs, Cancer Research, Vol. 59, No. 24, pp. 6080-6086, Dec 15, 1999. (journal site)
Tetsuo Shibuya, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and Kenji Tenmoku, Finding Useful Detours in Geographical Databases, IEICE Transactions on Information and Systems, Vol. E82-D, No. 1, pp. 282-290, January 1999. (journal site) (PDF file)
Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence Alignment, Journal of Computational Biology, Vol. 4, No. 3, Mary Ann Liebert, Inc., pp. 385-413, 1997. (preprint)

Refereed Conference Papers

Taku Onodera, Tetsuo Shibuya, Fast Classification of Protein Structures by an Alignment-free Kernel, The 23rd International Symposium on String Processing and Information Retrieval (SPIRE 2016), LNCS 9954, pp. 68-79, October 18-20, Beppu, Japan, 2016, DOI: 10.1007/978-3-319-46049-9_7
Yang Li, Tetsuo Shibuya, Malphite: A Convolutional Neural Network and Ensemble Learning Based Protein Secondary Structure Predictor, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), November 2015, pp. 1260-1266, IEEE Press, ISBN 978-1-4673-6799-8/15. doi:10.1109/BIBM.2015.7359861
Yoichi Sasaki, Tetsuo Shibuya, Kimihito Ito, and Hiroki Arimura, Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score, 8th International Conference on Similarity Search and Applications (SISAP 2015), October 12-14, Glasgow, Scotland, UK, 2015, LNCS 9371, pp. 191-203 (DOI: 10.1007/978-3-319-25087-8_18).
Mohammad A. Eita, Tetsuo Shibuya, and Amin A. Shoukry, Locating Controlling Regions of Neural Networks Using Constrained Evolutionary Computation, 2015 IEEE Congress on Evolutionary Computation (CEC2015), pp. 1581-1588, IEEE Press, ISBN 978-1-4799-7492-4/1, 2015, Sendai, Japan.
Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya and Masao Nagasaki, SVEM: a Structural Variant Estimation Method using Multi-Mapped Reads on Breakpoints, 1st International Conference on Algorithms for Computational Biology (AlCoB 2014), 2014, LNBI 8542, pp 208-219, 2014.
Sherin Moustafa El Gokhy, Tetsuo Shibuya and Amin Shoukry, Improving miRNA Classification Using an Exhaustive Set of Features, The 8th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB 2014), Advances in Intelligent Systems and Computing, Springer, Vol. 294, pp 31-39, 2014. (DOI: 10.1007/987-3-319-07581-5_4)
Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Detecting Superbubbles in Assembly Graphs, The 13th Workshop on Bioinformatics (WABI 2013), LNCS 8126, pp. 338-348, 2013.
Taku Onodera, Tetsuo Shibuya, The Gapped Spectrum Kernel for Support Vector Machines, Proc. Machine Learning and Data Mining (MLDM 2013), LNCS 7988, pp. 1-15, 2013.
Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Succinct de Bruijn Graphs, The 12th Workshop on Algorithms in Bioinformatics (WABI 2012), LNCS 7534, pp. 225-235, 2012.
Mohammed Sahli and Tetsuo Shibuya, Argan - an artificial sequencing tool for simulated data, The 4th International Conference on Bioinformatics and Biomedical Technology (ICBBT 2012), Vol. 29, pp. 196-199, 2012. (conference site)
Mohammed Sahli and Tetsuo Shibuya, An algorithm for classifying DNA reads, International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2012), Vol. 31, pp. 59-63, 2012. (conference site)
Mohammed Sahli and Tetsuo Shibuya, Qamar - A More Accurate DNA Sequencing Error Correcting Algorithm, International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2012), Vol. 31, pp. 53-58, 2012. (conference site)
Taku Onodera and Tetsuo Shibuya, An Index Structure for Spaced Seed Search, Proc. 22nd annual International Symposium on Algorithms and Computation (ISAAC 2011), LNCS, vol. 7074, pp. 764-772, 2011.
Daisuke Kimura, Tetsuji Kuboyama, Tetsuo Shibuya, and Hisashi Kashima, A Subpath Kernel for Rooted Unordered Trees, Proc. The 15th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2011), pp. 62-74, 2011. (Accepted as a long presentation paper)
Tetsuo Shibuya, Jesper Jansson and Kunihiko Sadakane, Linear-Time Protein 3-D Structure Searching with Insertions and Deletions, 9th Workshop on Algorithms in Bioinformatics (WABI 2009), LNCS, vol. 5724, pp. 310-320, 2009. (PDF file)
Ritsuko Onuki, Tetsuo Shibuya and Minoru Kanehisa, New Kernel Methods for Phenotype Prediction from Genotype Data, Proc. 9th Annual Workshop on Bioinformatics and Systems Biology (IBSB), Genome Informatics, Vol. 22, pp. 132-141, 2009. (PDF file)
Tetsuo Shibuya, Searching Protein 3-D Structures in Linear Time, Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), LNCS 5817 (LNBI 5541), pp. 1-15, 2009. (PDF file) (Best Paper Award)
Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, Proc. 14th String Processing and Information Retrieval Symposium (SPIRE 2007), LNCS 4726, pp. 300-309, 2007. (PDF file)
Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures, Proc. Combinatorial Pattern Matching 2006 (CPM 2006), LNCS 4009, pp. 84-93, 2006. (PDF file)
Hiroki Sakai, Hiroo Murakami, Sachiyo Aburatani, Tetsuo Shibuya, Katsuhisa Horimoto, and Minoru Kanehisa, Bayesian Approach for Sequence Pattern Search in Tissue Specific Alternative Splicing, Proc. 9th World Multi-Conference on Systemics, Cybernetics and Informatics, Vol. 3, pp. 25-30, 2005.
Tetsuo Shibuya and Igor Kurochkin, Match Chaining Algorithms for cDNA Mapping. Proc. Algorithms in Bioinformatics (WABI'03), LNCS 2182, pp. 462-473, 2003. (PDF file)
Kunihiko Sadakane and Tetsuo Shibuya, Indexing Huge Genome Sequences for Solving Various Problems. Genome Informatics, Vol. 12, pp. 175-183, 2001. (PDF file)
Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern Matching, Proc. 7th Scandinavian Workshop on Algorithm Theory (SWAT'00), LNCS 1851, pp. 393-406, 2000.
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, Proc. 10th annual International Symposium on Algorithms and Computation (ISAAC'99), LNCS 1741, pp. 225-236, 1999.
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently, Proc. 1st International Workshop on Algorithm Engineering and Experimentation (ALENEX'99), LNCS 1619, pp. 210-225, 1999.
Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, Proc. 10th ACM-SIAM Symposium on Discrete Algorithms (SODA 99), pp. 527-536, 1999.
Tetsuo Shibuya and Hiroshi Imai, New Flexible Approaches for Multiple Sequence Alignment, Proc. 1st Annual International Conference on Computational Molecular Biology (RECOMB '97), pp. 267-276, 1997.
Tetsuo Shibuya and Hiroshi Imai, Enumerating Suboptimal Alignments of Multiple Biological Sequences Efficiently, Proc. Pacific Symposium on Biocomputing '97, pp. 409-420, 1997.
Tetsuo Shibuya and Hiroshi Imai, Parametric Alignment of Multiple Biological Sequences, Genome Informatics, Vol 7, pp. 41-50, 1996.
Tetsuo Shibuya, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and Kenji Tenmoku, Detour Queries in Geographical Databases for Navigation and Related Algorithm Animations, Proc. International Symposium on Cooperative Database Systems for Advanced Applications (CODAS'96), Vol. 2, pp. 333-340, 1996.
Tsuyoshi Ono, Yoshiaki Kyoda, Tomonari Masada, Kazuyoshi Hayase, Motoki Nakade, Kunihiko Sadakane, Tetsuo Shibuya, Mary Inaba, Hiroshi Imai, Keiko Imai, and David Avis, A Package for Traiangulations. Proc. 12th Annual ACM Symposium on Computational Geometry, pp. V17-V18, 1996.
Tetsuo Shibuya, Takahiro Ikeda, Hiroshi Imai, Shigeki Nishimura, Hiroshi Shimoura, and Kenji Tenmoku, Finding a Realistic Detour by AI Search Techniques, Proc. 2nd Intelligent Transportation Systems, Vol. 4, pp. 2037-2044, 1995.

Books

Tetsuo Shibuya, Algorithms, Maruzen, 2016. (In Japanese. See my Japanese publication list)
Kengo Kinoshita, Tetsuo Shibuya, and Kenta Nakai, "Computational Biology", Gendai Suuri Kagaku Jiten, Heisuke Hiranaka eds., 2009, .pp. 342-354. (In Japanese. See my Japanese publication list)
Neil C.Jones and Pavel Pevzner, Introduction to Bioinformatics Algorithms, translated to Japanese by Tetsuo Shibuya and Hideo Bannai, 2007. (publisher's site) (Japanese Translation. See my Japanese publication list)
Kenta Nakai, et al. eds., Encyclopedia of Bioinformatics, Kyoritsu Shuppan, 2006. (In Japanese, as an editor and an author, , see my Japanese publication list). (publisher's site)
Tetsuo Shibuya, Basics of Datamining in Bioinformatics, Genome Kenkyuu Jikken Handbook, pp. 45-48, Yodosha, 2004. (In Japanese. See my Japanese publication list). (publisher's site)

Book Editor/Guest Editorial

Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai: Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014). IEEE/ACM Trans. Comput. Biology Bioinform. 12(4): 761-762 (2015).
Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai: Editorial. J. Bioinformatics and Computational Biology 12(6) (2014)
Tetsuo Shibuya, Hisashi Kashima, Jun Sese, and Shandar Ahmad (Eds): Pattern Recognition in Bioinformatics - 7th IAPR International Conference, PRIB 2012. LNCS 7632, Springer, 2012.

Invited Journal Articles

Tetsuo Shibuya, Faster Big Data Searching via Statistical Model-based Algorithm Design, Journal of the Institute of Electronics, Information and Communication Engineers, vol. 97, No. 5, May 2014, pp. 384-387. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Current Bioinformatics and Its Future, Journal of the Institute of Electronics, Information and Communication Engineers, vol. 90, no. 2, 2007, pp. 145-147. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, BDGF Method, Bio Venture, 2(6), pp. 86-89, 2002. (In Japanese, see my Japanese publication list)

Keynotes/Invited Talks

Tetsuo Shibuya, Algorithmic Challenges for Bio Big Data, UTokyo-IITM Workshop, March 15th, 2017, Chennai, India.
Tetsuo Shibuya, Algorithm Design Paradigm Shift Needed for Bio Big Data, Genomic Medicine 2015, Ho Chi Minh, Vietnam, July 21, 2015.
Tetsuo Shibuya, Algorithmic Challenges to Bio Big Data, The 11th International Workshop on Advanced Genomics, Tokyo, Japan, May 22, 2015.
Tetsuo Shibuya, Designing Faster Algorithms For Big Data, UK-Japan Workshop on Big Data, Feburuary 6, 2014.
Tetsuo Shibuya, Protein Structure Comparison Algorithms, The 35th Annual Meeting of the Molecular Biology Society of Japan, December 13, 2012. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Large-Scale Informtaion Technologies for Next Generation Sequencers, The 56th Annual Meeting of the Japan Society of Human Genetics, November 10, 2011. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Statistical Model-based Algorithm Design Framework for Faster Protein Structure Database Searching, Keynote, The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi 2010), December 13-15, 2010.
Tetsuo Shibuya, Large-Scale Computation Platform for Cancer Whole Genome Analysis, The 55th Annual Meeting of the Japan Society of Human Genetics, October 28, 2010. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Next-Generation Cancer Genome Analysis Pipeline, 2nd NUS-UT Workshop on Computational Systems Biology, Plenary Lecture, Feburuary 2010.
Tetsuo Shibuya, Protein Structures and Combinatorial Pattern Matching. SIG FPAI-68, 2008. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Combinatorial Structural Pattern Matching, The Second Japan-Taiwan Bilateral Symposium on Bioinformatics, November 7-9, 2006.
Tetsuo Shibuya, Indexing Structures for Biomolecular Structures, The First Japan-Taiwan Bilateral Symposium on Bioinformatics, March 13-15, 2006.

Invited Seminar Talks

Tetsuo Shibuya, Algorithm-driven Science, Symposium on Mathematics, Algorithms, Compter Science, and Data Science, June 10, Tokyo, 2017. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Algorithms in the Big Genomic Data Era, The 46th Workshop, The 164th Committee on Genome Technology, Japan Society for the Promotion of Science, October 24, 2014. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Faster Protein Structure Database Searching by a New Indexing Data Structure, CREST Symposium, January 12, 2014. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Indexing Protein 3-D Structures for Faster Similarity Search, November 29-30, Exploring the Limits of Computation (ELC), November 29-30, 2013.
Tetsuo Shibuya, Indexing Protein 3-D Structures for Faster Structural Similarity Queries, Seminar at Bioinformatics Center, Institute for Chemical Research, Kyoto University, October 18, 2013.
Tetsuo Shibuya, Fast Indexing Methods for Protein 3-D Structure Searching, NII Shonan Seminar 29: Compact Data Structures for Big Data, 2013.
Tetsuo Shibuya, Future Algorithm Design for Indexing in the Genome Big-Data Era, GCOE Seminar, Decipherring Biosphere from Genome Big Bang, March 1, 2013. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Succinct Representations of Assembly Graphs, The 164th Committee on Genome Technology, Japan Society for the Promotion of Science, January 11, 2013.
Tetsuo Shibuya, Statistical Models and Large-Scale Pattern Matching Algorithms, Minato Discrete Structure Manipulation System Project Seminar, January 20, 2012. (In Japanese, see my Japanese publication list)
Akihiro Fujimoto, Tetsuo Shibuya, "Information Analysis at the ICGC", The 34th Workshop, The 164th Committee on Genome Technology, Japan Society for the Promotion of Science, September 10, 2010. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, A New Algorithm Design Framework for Searching Protein 3-D Structures, GCOE (Decipherring Biosphere from Genome Big Bang) Special Lecture, 2010. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Combinatorial Pattern Matching for Protein 3-D Structures, SEQUOIA seminar, INRIA, 2008.
Tetsuo Shibuya, Indexing Technologies and Its Application to Gene Finding, Seimei-Jouhou-Kagaku Special Seminar, CBRC, Advanced Industrial Science and Technology, November 20, 2002. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, Pattern Discovery and Mining in Large Databases, BioEXPO 2002. Senmon-Gijutsu Seminar, July 12, 2002. (In Japanese, see my Japanese publication list)
Tetsuo Shibuya, New Approaches to Flexible Alignment of Multiple Biological Sequences, Combinatorial Optimization Seminar: Theory and Applications (COSTA), 97-4, October 25, 1997. (In Japanese, see my Japanese publication list)

Invited Conference Panel Discussions

Antonia Kwan, Satoru Miyano, Yasushi Okazaki and Tetsuo Shibuya, What are the applications and limitations of microarray datamining for immunology? First International Immunoinformatics Symposium, Feburuary 26, 2004.

Refereed Conference Posters

Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, Haplotype Inference Probability-based Genotype Clustering, Proc. 7th Annual Workshop on Bioinformatics and Systems Biology (IBSB), Genome Informatics, Vol. 18, pp. 26-27, 2007.
Makoto Kano, Hisashi Kashima, Tetsuo Shibuya, Kaori Ide, Aiko Kashihara, Noriko Nakagawa, Seiki Kuramitsu, Mariko Hatakeyama, and Akihiko Konagaya, Method for Normalization of Gene Expression Data, Genome Informatics, Vol. 14, p. 336-337, 2003.
Tetsuo Shibuya and Hiroshi Imai, Suboptimal Alignments of Multiple Biological Sequences. Intelligent Systems on Molecular Biology '96, Book of Abstracts, p. 76, June 1996.

Non-refereed Technical Reports / Talks

Sasaki et al, IPSJ, 2017. (In Japanese, see Japanese publications)
Taku Onodera, Tetsuo Shibuya, LA 2016, July 20, 2016, Nara. (In Japanese, see Japanese publications)
Yang Li, Tetsuo Shibuya, Malphite: A Convolutional Neural Network and Ensemble Learning Based Protein Secondary Structure Predictor, IPSJ SIG Technical Report, 2015-BIO-44(1), December 7, 2015.
Yoichi Sasaki, Tetsuo Shibuya, Kimito Ito, Hiroki Arimura, Efficient Approximate 3-Dimensional Point Set Matching and Its Application to Molecular Pattern Matching, IPSJ SIG Technical Report, 2015-BIO-42(68), pp. 1-7, June 15, 2015. (SIGBIO Best Student Presentation Award)
Taku Onodera, Kunihiko Sadakane, and Tetsuo Shibuya, Detecting Superbubbles in Assembly Graphs, IPSJ SIG Technical Report, 2013-BIO-35(4), 2013
Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, A New Implementation of Succinct de Bruijn Graphs, The 6th Annual Meeting of Asian Association for Algorithms and Computation, 2013.
Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Experimental Results on Succinct de Bruijn Graphs, The 16th Korea-Japan Joint Workshop on Algorithms and Computation, 2013.
Taku Onodera and Tetsuo Shibuya, IPSJ SIG Technical Report, 2012-BIO-31(4), 2012.
Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Compression of de Bruijn graphs, Technical Report of IEICE, COMP, September 2012.
Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Implementation of Succinct de Bruijn Graphs, Proc. 3rd Workshop on Algorithms for Large-Scale Information Processing (ALSIP 2012), 2012.
Taku Onodera and Tetsuo Shibuya, An Index Structure for Spaced Seed Search, IPSJ SIG Technical Report, 2011-AL-137(2), 2011.
Tetsuo Shibuya, Linear-Time Algorithm for Searching Protein 3-D Structures, IPSJ SIG Notes SIGAL 123-4, pp. 25-32, 2009.
Koichi Suematsu, Tetsuo Shibuya, Flexible Protein Alignment of 3D-Structures Allowing Dynamic Transformation, ISPSJ SIG Notes SIGBIO 12-12, pp. 87-94, 2008.
Tetsuo Shibuya, Efficient Substructure RMSD Query Algorithms, IPSJ SIG Notes SIGAL 114-8, pp. 57-64, 2007.
Tetsuo Shibuya, Fast and Accurate Algorithms for Protein Hinge Detection, IPSJ SIG Notes SIGBIO 10-4, pp. 25-32, 2007.
Tetsuo Shibuya, Prefix-Shuffled Geometric Suffix Tree, IPSJ SIG Notes SIGAL 112-1, 2007, pp. 1-8.
Kohichi Suematsu, Michihiro Araki, and Tetsuo Shibuya, Graph tiling algorithm for molecular synthesis analysis, SIGAL 106-4, pp. 25-32, 2006.
Tetsuo Shibuya, Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures, IPSJ SIG Notes SIGAL 105-3, pp. 17-24, 2006.
Tetsuo Shibuya, and Igor Kurochkin, Match Chaining Algorithms for cDNA Mapping. Technical Report of IEICE, Vol. 103, No. 326, COMP2003-37, pp. 1-8, 2003.
Tetsuo Shibuya, Christian Schoenbach, Hisashi Kashima and Akihiko Konagaya, Accurate cDNA Clustering Algorithm based on Spliced Sequence Alignment, Technical Report of IEICE, COMP2002-11, pp. 17-24, May 26, 2002.
Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt and Tetsuo Shibuya, The IBM Bioinformatics Group Web Server - Tools and Content, IBM Technical Report RC22726, 2002
Tetsuo Shibuya and Isidore Rigoutsos, Motif Search Algorithm and Its Applications for Gene Finding, Technical Report of IEICE, Vol. 101, No. 376, COMP2001-48, pp. 85-92, 2001.
Tetsuo Shibuya and Isidore Rigoutsos, Dictionary-driven Microbial Gene Finding, IBM Technical Report RC22051, 2001.
Tetsuo Shibuya, Generalization of a Suffix Tree for RNA Structural Pattern Matching, IBM TRL Report RT0342, 2000.
Tetsuo Shibuya, New Approaches for Analyzing Recombinations of Biological Sequences, IBM TRL Report RT0343, 2000.
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, IPSJ SIG Notes SIGAL 69-4, pp. 25-32, 1999.
Tetsuo Shibuya, New Approaches for Analyzing Recombinations of Biological Sequences, Technical Report of IEICE, Vol. 99, No. 30, COMP99-1, pp. 1-8, 1999.
Hiroshi Kawazoe, Tetsuo Shibuya, Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, IBM TRL Report RT0317, 1999.
Tetsuo Shibuya, Constructing the Suffix Tree of a Tree with a Large Alphabet, IBM TRL Report RT0320, 1999.
Hiroshi Kawazoe, Tetsuo Shibuya, and Takeshi Tokuyama, Optimal On-line Algorithms for an Electronic Commerce Money Distribution System, Technical Report of IEICE, Vol. 98, No. 283, COMP98-32, pp. 17-24, 1998.
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently By Using the A* Algorithm, IPSJ SIG Notes SIGAL 62-2, pp. 9-16, 1998.
Tetsuo Shibuya and Hiroshi Imai, New Approaches to Flexible Alignment of Multiple Biological Sequences, Cooperative Research Report, "Modeling and Algorithms 9", The Institute of Statical Mathematics, 1997.
Tetsuo Shibuya, Computing the n x m Shortest Paths Efficiently By Using the A* Algorithm, IBM TRL Report RT5133. 1997.
Tetsuo Shibuya and H. Imai, On Parametric Alignments of Multiple Biological Sequences, IPSJ SIG Notes SIGAL52-4, IPSJ, pp. 25-32, 1996, In Japanese.
Tetsuo Shibuya and Hiroshi Imai, Suboptimal Alignments of Multiple Biological Sequences, IPSJ SIG Notes SIGAL51-1, IPSJ, pp. 1-8, 1996.
Hiroshi Imai and Tetsuo Shibuya, K-opt Algorithm for Multiple Alignment, Cooperative Research Report, "Modeling and Algorithms 8", The Institute of Statical Mathematics, 1996.
Tetsuo Shibuya, Finding the k Shortest Paths by AI Search Techniques, Cooperative Research Report, "Modeling and Algorithms 7", The Institute of Statical Mathematics, Vol.77, pp. 212-222, 1995.

Non-refereed Poster Presentation

Kiyoshi Yamaguchi, Mitsuhiro Komura, Eigo Shimizu, Shinichi Kasuya, Rui Yamaguchi, Tetsuo Shibuya, Seiya Imoto, Satoshi Nagayama, Norihiko Takahashi, Tsuneo Ikenoue, Sumio Sugano, Satoru Miyano, Yoichi Furukawa, Search for pathogenic variants in familial colorectal cancer using a next generation sequencer, The 73rd Annual Meeting of the Japanese Cancer Association, S20-4, 2014.
Alexander Bowe, Taku Onodera, Kunihiko Sadakane and Tetsuo Shibuya, Implementation of Succinct de Bruijn Graphs, The 12th Workshop on Algorithms in Bioinformatics, 2012.
Akihiro Fujimoto, Hidwaki Nakagawa, Naoya Hosono, Kaoru Nakano, Tetsuo Abe, Masao Nagasaki, Rui Yamaguchi, Tetsuo Shibuya, Michiaki Kubo, Satoru Miyano, Usuke Nakamura and Tatsuhiko Tsunoda, Construction of analysis pipeline and accurate variant calls of a Japanese individual using massively parallel sequencing, The 2nd Biosupercomputing symposium, P-52, p. 146, 2010.
Tetsuo Shibuya, Faster Structural Pattern Matching Algorithms, The 9th International Workshop on Bioinformatics and Systems Bilogy, 2009.
Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, A New Method for Genotype Clustering based on Haplotype Inference, Biochemistry and Molecular Biology (BMB 2007), 1P-1071, 2007.
Ritsuko Onuki, Tetsuo Shibuya, and Minoru Kanehisa, Genotype Clustrering based on Haplotype Inference Probabilities, The 52nd Annual Meeting of the Japan Society of Human Genetics, 2007.
Yoshihiro Ohta and Tetsuo Shibuya, Extracting Causalities in Large Biological Data Sets, Japanese Society of Molecular Biology, 1998 Annual meeting, December 1999, Yokohama.

Theses

Tetsuo Shibuya, Research on Fast Algorithms for Comparison and Indexing of Biological Sequence Information, Ph. D Thesis, Department of Information Science, Faculty of Science, University of Tokyo, December 2002. (UT Repository)
Tetsuo Shibuya, New Approaches to Flexible Alignment of Multiple Biological Sequences, Master Thesis, Deptartment of Infomation Science, Faculty of Science, University of Tokyo, February 1997.
Tetsuo Shibuya, Finding the k shortest paths by AI search techniques. Bachelor Thesis, Deptartment of Infomation Science, Faculty of Science, University of Tokyo, February 1995.

Others

Publications in Japanese
List of patents (In Japanese)
List of newspaper articles (In Japanese)
List of papers of students in our laboratory